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comparison codon_usage.xml @ 8:71fd72235543 draft

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Uploaded 20181212
author fabio
date Wed, 12 Dec 2018 03:53:55 -0500
parents 5b61f1b564b3
children
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7:a625bcf76ce6 8:71fd72235543
1 <tool id="codon_usage" name="Codon Usage" version="0.2.0"> 1 <?xml version="1.0"?>
2 <tool name="Codon Usage" id="codon_usage" version="0.2.0">
2 <description>for each sequence in a file</description> 3 <description>for each sequence in a file</description>
3 <requirements> 4 <requirements>
4 <requirement type=“package” version=“3.6.0”>python</requirement> 5 <requirement type="package" version="3.6.0">python</requirement>
5 <requirement type=“package” version=“1.72”>biopython</requirement> 6 <requirement type="package" version="1.72">biopython</requirement>
6 <requirement type=“package” version=“0.23.4”>pandas</requirement> 7 <requirement type="package" version="0.23.4">pandas</requirement>
7 </requirements> 8 </requirements>
8 9
9 <command>python $__tool_directory__/codon_usage.py -i $input -t $input_type -o $output -c $codon_table</command> 10 <command>
11 <![CDATA[
12 python '$__tool_directory__/codon_usage.py' -i $input -t $input_type -o $output -c $codon_table
13 ]]>
14 </command>
10 <inputs> 15 <inputs>
11 <param name="input" format="fasta" type="data" label="Source file"/> 16 <param name="input" format="fasta" type="data" label="Source file"/>
12 17
13 <param name="input_type" type="select" format="text"> 18 <param name="input_type" type="select" format="text">
14 <label>Indicate the input file format</label> 19 <label>Indicate the input file format</label>
19 <param name="codon_table" type="select" format="text"> 24 <param name="codon_table" type="select" format="text">
20 <label>Choose the proper codon table for your organism)</label> 25 <label>Choose the proper codon table for your organism)</label>
21 <option value="Archaeal"> Archaeal</option> 26 <option value="Archaeal"> Archaeal</option>
22 <option value="Bacterial">Bacterial</option> 27 <option value="Bacterial">Bacterial</option>
23 <option value="Standard">Standard</option> 28 <option value="Standard">Standard</option>
24
25 </param> 29 </param>
26 </inputs> 30 </inputs>
27 31
28 <outputs> 32 <outputs>
29 <data format="tabular" name="output" /> 33 <data format="tabular" name="output" />